scPDB - 3kr4 entry

Protein Data Bank Entry:

PDB ID : 3kr4

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2009-11-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	M17 leucyl aminopeptidase
ID:	Q8IL11_PLAF7
AC:	Q8IL11
Organism:	Plasmodium falciparum
Reign:	Eukaryota
TaxID:	36329
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
B	100 %

Ligand binding site composition:

B-Factor:	13.203
Number of residues:	35
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	2
Water Molecules:	2
Cofactors:
Metals:	ZN MG

Cavity properties

Ligandability	Volume (Å3)
0.785	698.625

% Hydrophobic	% Polar
43.96	56.04
According to VolSite

Ligand :

HET Code:	BES
Formula:	C16H24N2O4
Molecular weight:	308.373 g/mol
DrugBank ID:	DB03424
Buried Surface Area:	63.4 %
Polar Surface area:	117.1 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	3
Rings:	1
Aromatic rings:	1
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
101.963	63.2592	10.8515

Binding mode :

What is Poseview ?

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Image generated by PoseView

Protein

Binding Site

Ligand

Interaction pattern

hydrophobic (CA)

aromatic (CZ)

hydrogen bond acceptor (O)

hydrogen bond acceptor/donor (OG)

hydrogen bond donor (N)

positively ionized (NZ)

negatively ionized (OD1)

metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
O3	NZ	LYS- 386	2.9	140.59	H-Bond (Protein Donor)	false
C9	CE	MET- 392	3.8	0	Hydrophobic	false
C11	CE	MET- 392	4.27	0	Hydrophobic	false
C9	CE	MET- 396	3.5	0	Hydrophobic	false
C11	CZ	PHE- 398	3.37	0	Hydrophobic	false
C15	CB	ASN- 457	4.36	0	Hydrophobic	false
C13	CB	ALA- 460	4.4	0	Hydrophobic	false
C15	CB	ALA- 460	4.02	0	Hydrophobic	false
N2	O	THR- 486	3.28	162.85	H-Bond (Ligand Donor)	false
N1	O	LEU- 487	3.18	134.79	H-Bond (Ligand Donor)	false
O1	N	GLY- 489	2.88	170.48	H-Bond (Protein Donor)	false
C16	CG2	ILE- 547	4.3	0	Hydrophobic	false
C16	CB	SER- 554	4.32	0	Hydrophobic	false
C12	CB	ALA- 577	3.83	0	Hydrophobic	false
O2	ZN	ZN- 1001	2.36	0	Metal Acceptor	false
O2	MG	MG- 1004	2.08	0	Metal Acceptor	false